2Q9H

Crystal structure of the C73S mutant of diaminopimelate epimerase

Summary for 2Q9H

• Entry DOI: 10.2210/pdb2q9h/pdb
• Related: 1BWZ 1GQZ 2GKE 2GKJ
• Descriptor: Diaminopimelate epimerase, L(+)-TARTARIC ACID, ACETIC ACID, ... (4 entities in total)
• Functional Keywords: c73s mutant, two structurally equivalent domains, apo form has an open conformation, isomerase
• Biological source: Haemophilus influenzae
• Cellular location: Cytoplasm: P44859
• Total number of polymer chains: 1
• Total formula weight: 30533.60

Authors

Pillai, B.,Cherney, M.,Diaper, C.M.,Sutherland, A.,Blanchard, J.S.,Vederas, J.C.,James, M.N.G. (deposition date: 2007-06-12, release date: 2007-10-23, Last modification date: 2023-08-30)

Primary citation

Pillai, B.,Cherney, M.,Diaper, C.M.,Sutherland, A.,Blanchard, J.S.,Vederas, J.C.,James, M.N.G.
Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase.
Biochem.Biophys.Res.Commun., 363:547-553, 2007

PubMed Abstract: Diaminopimelate (DAP) epimerase catalyzes the stereoinversion of ll-DAP to meso-DAP, a precursor of l-lysine and an essential component of the bacterial peptidoglycan. This function is vital to bacteria and the enzyme therefore represents an attractive target for the design of novel anti-bacterials. DAP epimerase belongs to the group of PLP-independent amino acid racemases that function through a rather unusual mechanism involving two cysteines acting in concert as a base (thiolate) and an acid (thiol). We have solved the crystal structures of the apo-forms of DAP epimerase mutants (C73S and C217S) from Haemophilus influenzae at 2.3A and 2.2A resolution, respectively. These structures provide a snapshot of the enzyme in the first step of the catalytic cycle. Comparisons with the structures of the inhibitor-bound form reveal that the enzyme adopts an 'open conformation' in the absence of substrates or inhibitors with the two active site cysteines existing as a thiol-thiolate pair. Substrate binding to the C-terminal domain triggers the closure of the N-terminal domain coupled with tight encapsulation of the ligand, stabilization of the conformation of an active site loop containing Cys73 and expulsion of water molecules with concomitant desolvation of the thiolate base. This structural rearrangement is critical for catalysis.

PubMed: 17889830
DOI: 10.1016/j.bbrc.2007.09.012

Experimental method

X-RAY DIFFRACTION (2.3 Å)